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[Bioc-devel] pushing changes to an existing package

9 messages · Simina Boca, Turaga, Nitesh

#
Thank you Nitesh and sorry for missing this initially!

This one seems fine:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> git remote -v
origin  https://github.com/SiminaB/MultiMed.git (fetch)
origin  https://github.com/SiminaB/MultiMed.git (push)
upstream        git at git.bioconductor.org:packages/MultiMed.g (fetch)
upstream        git at git.bioconductor.org:packages/MultiMed.g (push)

However, it seems like I only have read, not write access to the package:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> ssh -T
git at git.bioconductor.org | grep MultiMed
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
 R      packages/MultiMed

Cheers,
Simina



On Tue, Apr 30, 2019 at 11:01 AM Turaga, Nitesh <
Nitesh.Turaga at roswellpark.org> wrote:

            

  
    
#
Hi Simina,

We are going through the release process for Bioc 3.9 now, so all commits are blocked until further notice.

I can get back to helping you debug this issue once we are done with the release.

https://stat.ethz.ch/pipermail/bioc-devel/2019-May/015050.html

Best,

Nitesh
On May 2, 2019, at 12:58 PM, Simina Boca <smb310 at georgetown.edu<mailto:smb310 at georgetown.edu>> wrote:
Thank you Nitesh and sorry for missing this initially!

This one seems fine:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> git remote -v
origin  https://github.com/SiminaB/MultiMed.git (fetch)
origin  https://github.com/SiminaB/MultiMed.git (push)
upstream        git at git.bioconductor.org<mailto:git at git.bioconductor.org>:packages/MultiMed.g (fetch)
upstream        git at git.bioconductor.org<mailto:git at git.bioconductor.org>:packages/MultiMed.g (push)

However, it seems like I only have read, not write access to the package:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> ssh -T git at git.bioconductor.org<mailto:git at git.bioconductor.org> | grep MultiMed
Warning: Permanently added 'git.bioconductor.org<http://git.bioconductor.org/>,34.192.48.227' (ECDSA) to the list of known hosts.
 R      packages/MultiMed

Cheers,
Simina
On Tue, Apr 30, 2019 at 11:01 AM Turaga, Nitesh <Nitesh.Turaga at roswellpark.org<mailto:Nitesh.Turaga at roswellpark.org>> wrote:
Hi Simina,

http://bioconductor.org/developers/how-to/git/faq/ #14 to help us out a little more please.

Best,

Nitesh
On Apr 30, 2019, at 10:45 AM, Simina Boca <smb310 at georgetown.edu<mailto:smb310 at georgetown.edu>> wrote:
Hello,

I am trying to update my package MultiMed
https://www.bioconductor.org/packages/release/bioc/html/MultiMed.html. It's
on Github at https://github.com/SiminaB/MultiMed. I got and updated the SSH
key (since I am using a new computer) but when I try to "git fetch --all" I
still get a permission-related error:

C:\Users\smb310\Documents\GitNuh\Multimed [devel]> git fetch --all
Fetching origin
Fetching upstream
Warning: Permanently added 'git.bioconductor.org<http://git.bioconductor.org/>,34.172.43.227' <ECDSA> to
the list of known hosts.
FATAL: R any packages/MultiMed.g SiminaB DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the current access rights and the repository
exists.
error: Could not fetch upstream

I appreciate your help!

Cheers,
Simina


--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/


_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.


--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/




This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
#
No worries, thanks for letting me know!

Cheers,
Simina

On Thu, May 2, 2019, 1:02 PM Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>
wrote:

  
  
#
Hi Simina,

Now that the RELEASE_3_9 branch and pushes are available to everyone, I can help you with this.

It seems like your upstream branch is a little funny looking, is this how it got pasted in or maybe it's a mistake.

What you gave: (I understand that the mailto: stuff may have been added later but auto format settings in email, but the trailing "g" at the end of the line is bugging me and I can't help but think it might be that)

upstream        git at git.bioconductor.org<mailto:git at git.bioconductor.org><mailto:git at git.bioconductor.org>:packages/MultiMed.g (fetch)
upstream        git at git.bioconductor.org<mailto:git at git.bioconductor.org>:packages/MultiMed.g (push)

What it's supposed to be:

upstream       git at git.bioconductor<mailto:git at git.bioconductor>.org:packages/MultiMed.git (fetch)
upstream.      git at git.bioconductor<mailto:git at git.bioconductor>.org:packages/MultiMed.git (push)


You can try first by resetting your upstream,

git remote set-url upstream git at git.bioconductor<mailto:git at git.bioconductor>.org:packages/MultiMed.git

Let me know if this works.

Best,

Nitesh
On May 2, 2019, at 1:02 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org<mailto:Nitesh.Turaga at RoswellPark.org>> wrote:
Hi Simina,

We are going through the release process for Bioc 3.9 now, so all commits are blocked until further notice.

I can get back to helping you debug this issue once we are done with the release.

https://stat.ethz.ch/pipermail/bioc-devel/2019-May/015050.html

Best,

Nitesh
On May 2, 2019, at 12:58 PM, Simina Boca <smb310 at georgetown.edu<mailto:smb310 at georgetown.edu>> wrote:
Thank you Nitesh and sorry for missing this initially!

This one seems fine:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> git remote -v
origin  https://github.com/SiminaB/MultiMed.git (fetch)
origin  https://github.com/SiminaB/MultiMed.git (push)
upstream        git at git.bioconductor.org<mailto:git at git.bioconductor.org>:packages/MultiMed.g (fetch)
upstream        git at git.bioconductor.org<mailto:git at git.bioconductor.org>:packages/MultiMed.g (push)

However, it seems like I only have read, not write access to the package:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> ssh -T git at git.bioconductor.org<mailto:git at git.bioconductor.org> | grep MultiMed
Warning: Permanently added 'git.bioconductor.org<http://git.bioconductor.org/>,34.192.48.227' (ECDSA) to the list of known hosts.
R      packages/MultiMed

Cheers,
Simina
On Tue, Apr 30, 2019 at 11:01 AM Turaga, Nitesh <Nitesh.Turaga at roswellpark.org<mailto:Nitesh.Turaga at roswellpark.org>> wrote:
Hi Simina,

http://bioconductor.org/developers/how-to/git/faq/ #14 to help us out a little more please.

Best,

Nitesh
On Apr 30, 2019, at 10:45 AM, Simina Boca <smb310 at georgetown.edu<mailto:smb310 at georgetown.edu>> wrote:
Hello,

I am trying to update my package MultiMed
https://www.bioconductor.org/packages/release/bioc/html/MultiMed.html. It's
on Github at https://github.com/SiminaB/MultiMed. I got and updated the SSH
key (since I am using a new computer) but when I try to "git fetch --all" I
still get a permission-related error:

C:\Users\smb310\Documents\GitNuh\Multimed [devel]> git fetch --all
Fetching origin
Fetching upstream
Warning: Permanently added 'git.bioconductor.org<http://git.bioconductor.org/>,34.172.43.227' <ECDSA> to
the list of known hosts.
FATAL: R any packages/MultiMed.g SiminaB DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the current access rights and the repository
exists.
error: Could not fetch upstream

I appreciate your help!

Cheers,
Simina


--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/


_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.


--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/




This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
#
Once your access works you should see yourself as maintainer with Read and Write access on MultiMed and CancerMutationAnalysis.

Best

Nitesh 

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
#
Thank you, it seems to work now! Do you have any idea of why the ".git" had
been moved to ".g?" Just curious if it was something on my end.

Cheers,
Simina

On Thu, May 2, 2019 at 2:15 PM Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>
wrote:

  
    
#
No idea Simina.  Maybe a typo? 

Best,

Nitesh 


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
4 days later
#
Thank you again Nitesh! I'm now having some issues with pushing the origin
master:

C:\Users\smb310\Documents\GitHub\MultiMed [master ?]> git push upstream
master

Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.

Counting objects: 16, done.

Delta compression using up to 8 threads.

Compressing objects: 100% (16/16), done.

Writing objects: 100% (16/16), 2.48 KiB | 0 bytes/s, done.

Total 16 (delta 10), reused 0 (delta 0)

To git at git.bioconductor.org:packages/MultiMed.git

   9361279..5cc7187  master -> master

C:\Users\smb310\Documents\GitHub\MultiMed [master ?]> git push origin master

remote: Invalid username or password.

fatal: Authentication failed for 'https://github.com/SiminaB/MultiMed.git/'

C:\Users\smb310\Documents\GitHub\MultiMed [master ?]>

On Thu, May 2, 2019 at 2:49 PM Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>
wrote:

  
    
#
Hi Simina,

This is an issue with Github. So just to walk through what might be happening, this is a case when users set up 2FA (two factor authentication). You might want to to set up SSH keys for GitHub as well, and use the SSH protocol (given below instead of HTTPS) as your remote origin.

	git at github.com:SiminaB/MultiMed.git 

https://help.github.com/en/articles/connecting-to-github-with-ssh

Or if you've forgotten your GitHub password. 

Everything on the Bioc git server seems fine though.

Best,

Nitesh 

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.